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| Reflections on my first experience in scientific research [T Ryan Gregory's column] Posted: 03 May 2008 05:26 PM CDT I often tell undergraduates about the importance of conducting research projects in their senior year if they intend to pursue graduate studies in science. There are two main reasons for this. The first is that the labs that they have experienced up to that point in undergraduate courses, though useful for introducing specific concepts, are a poor reflection of what real science is like. As such, it is important for them to experience original lab work, rather than simply following a pre-defined, "cook book" protocol with an expected result. Novel studies have no pre-defined sequence, no a priori expectation of the outcome, and in many cases no established methods in place for generating data. The second is that there are some important lessons that they need to learn about research, perhaps most importantly that whatever they try to do in the lab will not work the first time. The sooner they hit that wall -- and get around it -- the better. Nature does not give up her secrets easily, I sometimes say. |
| if I had 3 trillion dollars... [the skeptical alchemist] Posted: 03 May 2008 03:57 PM CDT |
| Internal Medicine Journal Search: Personalize Your Searches! [ScienceRoll] Posted: 03 May 2008 01:20 PM CDT Have you ever heard about Google Co-op? According to Wikipedia:
Flavio Guzmán created his own search engine, the Internal Medicine Journal Search where we can search on the top 5 medical journals: JAMA, NEJM, BMJ, AIM and Lancet.
This is a great example on how to create a customized search engine. Another example is the Scienceroll Personalized Search Engine where you can choose which databases to search in. More about it here.         |
| Gene2MeSH: Automated Literature Based Genome Annotation [ScienceRoll] Posted: 03 May 2008 12:37 PM CDT Some weeks ago, I mentioned on Twitter how hard it is to find proper gene-disease associations in Pubmed, the database of health-science data. Some days later, P. F. Anderson sent me this link: Gene2MeSH.
I gave it a try and made a search for psoriasis:
It looks like an interesting and useful idea, while the MeSH heading column seems to be totally unnecessary, for example. I will keep on using it and will let you know how it goes. Further reading:         |
| What’s on the web (2008 May 3) [ScienceRoll] Posted: 03 May 2008 11:57 AM CDT
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| Tons of data everywhere. Do we need life science CDNs? [business|bytes|genes|molecules] Posted: 03 May 2008 11:00 AM CDT This weeks Bio-IT World meeting was all about data storage. Driven by the needs of integrating complex, heterogenous data and most of all by next gen sequencing, it’s amazing how much data the life sciences are generating and how poorly prepared we are. I won’t necessarily mention names, but there are places which have data hitting the petabytes AFTER throwing away most of it. How do you access this data? How do you back it up? What kind of data centers do you need? What kind of power do you need? When people are worried about the city being able to handle their power needs then there is cause for concern. It is also why I think the future of scientific data generation needs to be thought about like Google, etc view data, infrastructure and data access. What if we had a Big Table like distributed file system where all this data could be uploaded to? What data would be uploaded there? How would we access it? Ideally data from public genome projects would be made available as Open Data, available to everyone for downstream analysis under a CC0 or similar license. Of course there is a lot more to these data than just whole genome sequencing. There is also the challenge of just the pipes that the data needs to travel through. These are really large files. Whatever the solution(s), next gen sequencing and the resultant data glut were top of mind. And this is just the start. Personally, I think that those in small labs who want access to sequencers for their own work really need to reconsider. Their utilization rates are unlikely to justify the cost and they will almost certainly run into data storage, access and archiving issues, especially when something like PacBio comes online. A utility model works best here, a model where people get access to time on machines or access to machines hosted at core facilities, etc. The more I think about these issues, the more I am convinced that the life sciences really need to embrace something like CDNs. With the sheer volume and variety of data, we need people who can step up to the plate and provide the infrastructure instead of depending on a few people who aren’t necessarily thinking about data the way Google or Yahoo do on a daily basis (although the way it looks some of them are doing just that). I am especially worried about smaller groups and labs who might just get left out if we don’t develop the appropriate ecosystem. The economics of all this? That’s another issue for another day. Further reading  |
| 2 Women, One Prize, Oprah and a new Industry [The Gene Sherpa: Personalized Medicine and You] Posted: 03 May 2008 08:48 AM CDT The Albany Medical Center Prize in Medicine and Biomedical Research was recently awarded to 2 scientists for their work on snRNPs and Telomerase. Oh yes, that magical molecule that will allow us to... [[ This is a content summary only. Visit my website for full links, other content, and more! ]] |
| DNA Video: DNA Replication Song [Eye on DNA] Posted: 03 May 2008 03:07 AM CDT This DNA replication song set to Backstreet Boys is truly cringe worthy!
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| Ancestral effective population size [Mailund on the Internet] Posted: 03 May 2008 01:59 AM CDT John Hawks — in a discussion of a potential bottleneck in the human ancestral population — gives a good description of “effective population size” and how you go about inferring ancestral effective population sizes. Worth a read. |
| Fancy a peek inside Sanger's Illumina GA Pipeline? [SEQanswers.com] Posted: 02 May 2008 11:41 PM CDT So it has been brought to my attention that the Sanger has a publicly accessible "stats" page that contains quite a few statistics about their Illumina short read pipeline. The stats give a very interesting look into the daily operations of perhaps highest throughput genome center in the world (...if I had a nickel for every PM I will get correcting me! ). Screenshot of the public page, containing a dropdown menu for different stats: I have reproduced all the available data below,... Read more and join the community... |
| Researchers report the cloning of a key group of human genes, the protein kinases [Think Gene] Posted: 02 May 2008 10:12 PM CDT Although the human genome has been sequenced, research into mechanism of action of genes has been hampered by the fact that most human genes have not been isolated. This is true for even the most common class of cancer-associated genes, the protein kinases, which mediate the majority of signaling events in cells by phosphorylating and [...] |
| New ‘OPAL Therapy’ presents simple, cost-effective method of treating HIV infection [Think Gene] Posted: 02 May 2008 10:11 PM CDT Australian researchers have unveiled a new immunotherapy technique to help prevent the progression from HIV infection to AIDS. Details of the simple, cost-effective technique are published May 2nd in the open-access journal PLoS Pathogens. There is an overwhelming need for effective immunotherapies for HIV, as current therapies are expensive, impractical, and often highly toxic. The authors, [...] |
| Is A Biochemistry Major Too Hard? [adaptivecomplexity's column] Posted: 02 May 2008 09:38 PM CDT I missed this interesting discussion at Larry Moran's Sandwalk: Are biochemistry programs too hard compared to other biology majors? Larry says his biochemistry program is losing students to other biology majors that don't require as much physics and chemis |
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